[gmx-users] timestep fraction complete

Mark Abraham Mark.Abraham at anu.edu.au
Fri Sep 25 00:34:50 CEST 2009

Jack Shultz wrote:
> I figured out another way to update the progress of my simulation, but I 
> need to report the fraction of completion at the certain intervals of 
> mdrun. Possibly at every time step or if that does not make sense every 
> 100 timesteps. I don't think this is a feature currently supported, so I 
> will have to make some source code chages. I am looking for the 
> variables related to total number of time steps and where it controls 
> the the current time step so I can calculate the fraction of complete 
> where current-timestep / total-timestep

Under at least some circumstances GROMACS writes the expected runtime 
remaining to stderr, but I don't recall what/when. Piping that to some 
useful script has to be a good start. You certainly don't need this data 
every time step, and don't want to be perturbing mdrun to get it.

Even if the above was unsuitable, surely progress would only need to be 
moderately accurate and for simulations that last many hours. If so, 
you'll get good enough data by grepping a gmxdump of the .tpr to get the 
expected frequencies of output and length of run, and then watching the 
growth of whichever of .log/.trr/.edr is written most frequently. I/O 
buffering will affect the numbers somewhat.


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